Extended Data Fig. 11: Identification of compartments and differences between cell types.
From: Cell-type specialization is encoded by specific chromatin topologies
a, Open and closed chromatin compartments (A and B, respectively) display different genomic distributions in mES cells, OLGs, PGNs and DNs. Mouse replicates 1 and 2 (R1 and R2, respectively) are shown. Purple, compartment A; orange, compartment B. b, Comparison of compartment A/B membership in GAM datasets from PGNs and DNs and their replicates. Compartment changes show good overlap between replicates. Purple, compartment A; orange, compartment B. c, Pearson’s correlation of eigenvectors shows the largest differences between mES cells and brain cell types. d, UpSet plot showing all combinations of compartments changes Most genomic windows share membership to compartments A, followed by B, in all cell types. The most frequent compartment changes occur from compartment B in mES cells to A in all brain cells (pink box), followed by changes from A in mES cells to B in all brain cells (blue box). e, Compartment changes for each cell type comparison in each chromosome. Only compartments common to both replicates were used in the comparison. Brain cell types have higher overlap with each other as compared to mES cells. PGNs and DNs had the most overlap for most chromosomes. f, Violin plots of the distribution of compartment lengths show similar lengths between cell types. Right, percentage of the genome covered by A or B compartments in each cell type shows similar distribution between cell types.
